Starting phenix.real_space_refine on Fri Jul 3 09:17:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w01_32233/07_2026/7w01_32233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w01_32233/07_2026/7w01_32233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w01_32233/07_2026/7w01_32233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w01_32233/07_2026/7w01_32233.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w01_32233/07_2026/7w01_32233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w01_32233/07_2026/7w01_32233.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7w01_32233/07_2026/7w01_32233.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w01_32233/07_2026/7w01_32233.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 70 5.16 5 C 8287 2.51 5 N 2114 2.21 5 O 2251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12724 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1598, 12556 Classifications: {'peptide': 1598} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 74, 'TRANS': 1523} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 168 Unusual residues: {'NAG': 2, 'POV': 3, 'PX4': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 2.78, per 1000 atoms: 0.22 Number of scatterers: 12724 At special positions: 0 Unit cell: (102.6, 142.56, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 2 15.00 O 2251 8.00 N 2114 7.00 C 8287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1274 " - pdb=" SG CYS A1284 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1801 " - " ASN A 124 " " NAG A1802 " - " ASN A 140 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 609.6 milliseconds 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2992 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 12 sheets defined 48.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 removed outlier: 3.548A pdb=" N ALA A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 87 through 99 removed outlier: 3.549A pdb=" N THR A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 removed outlier: 4.137A pdb=" N ARG A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 225 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.560A pdb=" N GLN A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 272 removed outlier: 4.728A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Proline residue: A 264 - end of helix removed outlier: 3.663A pdb=" N SER A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.569A pdb=" N ARG A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 302 through 328 removed outlier: 3.560A pdb=" N LEU A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 365 removed outlier: 3.673A pdb=" N VAL A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 379 through 385 removed outlier: 4.141A pdb=" N PHE A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 400 through 408 Processing helix chain 'A' and resid 410 through 427 removed outlier: 3.610A pdb=" N ALA A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 474 removed outlier: 4.013A pdb=" N LEU A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 472 " --> pdb=" O TRP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'A' and resid 600 through 605 removed outlier: 3.657A pdb=" N ILE A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 634 removed outlier: 3.810A pdb=" N LEU A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 628 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 632 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 652 Processing helix chain 'A' and resid 669 through 679 removed outlier: 3.541A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 679 " --> pdb=" O ILE A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 710 removed outlier: 3.784A pdb=" N ILE A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 3.531A pdb=" N LEU A 729 " --> pdb=" O GLU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.695A pdb=" N LYS A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 781 removed outlier: 3.552A pdb=" N ILE A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 803 removed outlier: 4.029A pdb=" N THR A 803 " --> pdb=" O ARG A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 816 removed outlier: 3.796A pdb=" N LYS A 815 " --> pdb=" O ALA A 811 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 816 " --> pdb=" O LYS A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 843 removed outlier: 3.839A pdb=" N VAL A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 917 removed outlier: 4.079A pdb=" N HIS A 904 " --> pdb=" O GLY A 900 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP A 909 " --> pdb=" O CYS A 905 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 915 " --> pdb=" O MET A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 943 removed outlier: 4.044A pdb=" N LEU A 934 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 940 " --> pdb=" O CYS A 936 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 988 Processing helix chain 'A' and resid 1005 through 1015 removed outlier: 3.560A pdb=" N ILE A1009 " --> pdb=" O GLU A1005 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER A1013 " --> pdb=" O ILE A1009 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A1014 " --> pdb=" O PHE A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1023 Processing helix chain 'A' and resid 1048 through 1065 removed outlier: 3.615A pdb=" N THR A1052 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A1054 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1090 removed outlier: 3.501A pdb=" N ALA A1087 " --> pdb=" O ALA A1083 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.640A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A1103 " --> pdb=" O ASP A1099 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1104 " --> pdb=" O ILE A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1116 removed outlier: 3.880A pdb=" N PHE A1115 " --> pdb=" O ALA A1112 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A1116 " --> pdb=" O SER A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1125 removed outlier: 3.902A pdb=" N ARG A1123 " --> pdb=" O ALA A1119 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A1125 " --> pdb=" O SER A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1134 removed outlier: 3.804A pdb=" N VAL A1130 " --> pdb=" O GLN A1126 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A1131 " --> pdb=" O ALA A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1152 removed outlier: 3.935A pdb=" N TRP A1142 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A1144 " --> pdb=" O SER A1140 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A1147 " --> pdb=" O LEU A1143 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1167 removed outlier: 4.490A pdb=" N LEU A1161 " --> pdb=" O SER A1157 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1163 " --> pdb=" O LEU A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1173 removed outlier: 3.582A pdb=" N PHE A1172 " --> pdb=" O VAL A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1199 removed outlier: 3.859A pdb=" N LEU A1182 " --> pdb=" O MET A1178 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A1184 " --> pdb=" O ASP A1180 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1191 " --> pdb=" O LEU A1187 " (cutoff:3.500A) Proline residue: A1194 - end of helix Processing helix chain 'A' and resid 1200 through 1203 Processing helix chain 'A' and resid 1205 through 1230 removed outlier: 3.914A pdb=" N TYR A1210 " --> pdb=" O ALA A1206 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A1211 " --> pdb=" O ALA A1207 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A1215 " --> pdb=" O THR A1211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1223 " --> pdb=" O LEU A1219 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR A1224 " --> pdb=" O SER A1220 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A1228 " --> pdb=" O THR A1224 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A1230 " --> pdb=" O LEU A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1249 removed outlier: 3.573A pdb=" N HIS A1247 " --> pdb=" O LYS A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1274 removed outlier: 3.518A pdb=" N MET A1259 " --> pdb=" O HIS A1255 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A1260 " --> pdb=" O CYS A1256 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A1263 " --> pdb=" O MET A1259 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A1274 " --> pdb=" O THR A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1288 Processing helix chain 'A' and resid 1306 through 1311 Processing helix chain 'A' and resid 1315 through 1326 removed outlier: 3.799A pdb=" N ILE A1319 " --> pdb=" O CYS A1315 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A1320 " --> pdb=" O ALA A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1368 removed outlier: 3.513A pdb=" N ILE A1368 " --> pdb=" O GLU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1421 through 1430 removed outlier: 3.595A pdb=" N THR A1425 " --> pdb=" O GLY A1421 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE A1426 " --> pdb=" O LYS A1422 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS A1427 " --> pdb=" O THR A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1483 removed outlier: 3.820A pdb=" N LEU A1477 " --> pdb=" O GLY A1473 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A1480 " --> pdb=" O MET A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1502 removed outlier: 3.696A pdb=" N THR A1498 " --> pdb=" O CYS A1494 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A1500 " --> pdb=" O GLU A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1508 Processing helix chain 'A' and resid 1520 through 1525 removed outlier: 3.663A pdb=" N THR A1525 " --> pdb=" O ARG A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1563 removed outlier: 3.861A pdb=" N THR A1556 " --> pdb=" O LEU A1552 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A1561 " --> pdb=" O VAL A1557 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1580 removed outlier: 3.539A pdb=" N ALA A1579 " --> pdb=" O GLU A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1597 through 1606 Processing helix chain 'A' and resid 1619 through 1634 removed outlier: 5.252A pdb=" N GLU A1625 " --> pdb=" O GLN A1621 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A1626 " --> pdb=" O GLU A1622 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A1632 " --> pdb=" O LYS A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1673 removed outlier: 4.685A pdb=" N GLU A1671 " --> pdb=" O GLU A1667 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A1672 " --> pdb=" O LYS A1668 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A1673 " --> pdb=" O ALA A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1690 Processing helix chain 'A' and resid 1691 through 1696 removed outlier: 4.070A pdb=" N HIS A1694 " --> pdb=" O SER A1691 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A1696 " --> pdb=" O ALA A1693 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.587A pdb=" N THR A 241 " --> pdb=" O VAL A1038 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG A1035 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A1037 " --> pdb=" O ARG A1030 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 109 removed outlier: 3.546A pdb=" N ARG A 108 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLU A 79 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA A 132 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA A 81 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 151 Processing sheet with id=AA4, first strand: chain 'A' and resid 555 through 557 removed outlier: 6.803A pdb=" N LEU A 556 " --> pdb=" O GLY A 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 535 through 537 removed outlier: 7.413A pdb=" N LYS A 537 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG A 550 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 609 through 611 removed outlier: 6.916A pdb=" N GLY A 609 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A 686 " --> pdb=" O VAL A 717 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN A 560 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU A 718 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR A 562 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 561 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ALA A 734 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 563 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N MET A 736 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS A 743 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 786 through 788 removed outlier: 3.627A pdb=" N SER A 788 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1387 through 1391 removed outlier: 6.524A pdb=" N LYS A1388 " --> pdb=" O ALA A1398 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A1396 " --> pdb=" O TYR A1390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1410 through 1412 Processing sheet with id=AB1, first strand: chain 'A' and resid 1415 through 1416 removed outlier: 6.871A pdb=" N LEU A1415 " --> pdb=" O MET A1587 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A1591 " --> pdb=" O VAL A1588 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1441 through 1442 removed outlier: 3.903A pdb=" N HIS A1445 " --> pdb=" O VAL A1442 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1614 through 1615 removed outlier: 3.743A pdb=" N ASP A1677 " --> pdb=" O LYS A1614 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3948 1.34 - 1.46: 2625 1.46 - 1.58: 6334 1.58 - 1.70: 4 1.70 - 1.82: 115 Bond restraints: 13026 Sorted by residual: bond pdb=" C29 POV A1806 " pdb="C210 POV A1806 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" C29 POV A1805 " pdb="C210 POV A1805 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.92e+01 bond pdb=" C29 POV A1807 " pdb="C210 POV A1807 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.92e+01 bond pdb=" C9 PX4 A1804 " pdb=" O5 PX4 A1804 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C9 PX4 A1803 " pdb=" O5 PX4 A1803 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.98e+01 ... (remaining 13021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 17343 3.40 - 6.81: 247 6.81 - 10.21: 29 10.21 - 13.61: 2 13.61 - 17.02: 7 Bond angle restraints: 17628 Sorted by residual: angle pdb=" C ILE A1233 " pdb=" N PRO A1234 " pdb=" CA PRO A1234 " ideal model delta sigma weight residual 119.84 128.00 -8.16 1.25e+00 6.40e-01 4.26e+01 angle pdb=" N ARG A 155 " pdb=" CA ARG A 155 " pdb=" C ARG A 155 " ideal model delta sigma weight residual 110.80 123.93 -13.13 2.13e+00 2.20e-01 3.80e+01 angle pdb=" CA ARG A 155 " pdb=" C ARG A 155 " pdb=" N PHE A 156 " ideal model delta sigma weight residual 116.84 127.00 -10.16 1.71e+00 3.42e-01 3.53e+01 angle pdb=" C28 POV A1806 " pdb=" C29 POV A1806 " pdb="C210 POV A1806 " ideal model delta sigma weight residual 127.79 110.77 17.02 3.00e+00 1.11e-01 3.22e+01 angle pdb=" C28 POV A1807 " pdb=" C29 POV A1807 " pdb="C210 POV A1807 " ideal model delta sigma weight residual 127.79 110.91 16.88 3.00e+00 1.11e-01 3.17e+01 ... (remaining 17623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 7523 33.87 - 67.73: 193 67.73 - 101.60: 17 101.60 - 135.47: 3 135.47 - 169.34: 1 Dihedral angle restraints: 7737 sinusoidal: 3101 harmonic: 4636 Sorted by residual: dihedral pdb=" CA ARG A 155 " pdb=" C ARG A 155 " pdb=" N PHE A 156 " pdb=" CA PHE A 156 " ideal model delta harmonic sigma weight residual 180.00 126.71 53.29 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA ASN A 140 " pdb=" C ASN A 140 " pdb=" N HIS A 141 " pdb=" CA HIS A 141 " ideal model delta harmonic sigma weight residual -180.00 -136.79 -43.21 0 5.00e+00 4.00e-02 7.47e+01 dihedral pdb=" CA PHE A 156 " pdb=" C PHE A 156 " pdb=" N SER A 157 " pdb=" CA SER A 157 " ideal model delta harmonic sigma weight residual 180.00 147.42 32.58 0 5.00e+00 4.00e-02 4.25e+01 ... (remaining 7734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1934 0.134 - 0.269: 45 0.269 - 0.403: 1 0.403 - 0.537: 0 0.537 - 0.672: 1 Chirality restraints: 1981 Sorted by residual: chirality pdb=" CA PHE A 156 " pdb=" N PHE A 156 " pdb=" C PHE A 156 " pdb=" CB PHE A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA PHE A1172 " pdb=" N PHE A1172 " pdb=" C PHE A1172 " pdb=" CB PHE A1172 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C7 PX4 A1804 " pdb=" C6 PX4 A1804 " pdb=" C8 PX4 A1804 " pdb=" O7 PX4 A1804 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1978 not shown) Planarity restraints: 2218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A1805 " 0.159 2.00e-02 2.50e+03 3.23e-01 1.04e+03 pdb=" C29 POV A1805 " -0.428 2.00e-02 2.50e+03 pdb="C210 POV A1805 " 0.428 2.00e-02 2.50e+03 pdb="C211 POV A1805 " -0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A1806 " -0.321 2.00e-02 2.50e+03 3.22e-01 1.04e+03 pdb=" C29 POV A1806 " 0.317 2.00e-02 2.50e+03 pdb="C210 POV A1806 " 0.328 2.00e-02 2.50e+03 pdb="C211 POV A1806 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A1807 " -0.102 2.00e-02 2.50e+03 1.03e-01 1.05e+02 pdb=" C29 POV A1807 " 0.101 2.00e-02 2.50e+03 pdb="C210 POV A1807 " 0.104 2.00e-02 2.50e+03 pdb="C211 POV A1807 " -0.103 2.00e-02 2.50e+03 ... (remaining 2215 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 19 2.35 - 2.99: 6685 2.99 - 3.63: 16998 3.63 - 4.26: 26611 4.26 - 4.90: 45763 Nonbonded interactions: 96076 Sorted by model distance: nonbonded pdb=" O VAL A 968 " pdb=" O GLN A 995 " model vdw 1.717 3.040 nonbonded pdb=" O THR A 966 " pdb=" CB GLU A 993 " model vdw 2.030 3.440 nonbonded pdb=" NE2 GLN A 613 " pdb=" OE1 GLU A 690 " model vdw 2.074 3.120 nonbonded pdb=" OD2 ASP A1149 " pdb=" OH TYR A1197 " model vdw 2.076 3.040 nonbonded pdb=" O LYS A 711 " pdb=" N ASP A 713 " model vdw 2.202 3.120 ... (remaining 96071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.190 13029 Z= 0.493 Angle : 1.112 17.015 17636 Z= 0.579 Chirality : 0.060 0.672 1981 Planarity : 0.011 0.323 2216 Dihedral : 15.952 169.336 4742 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.76 % Allowed : 13.30 % Favored : 85.94 % Rotamer: Outliers : 0.60 % Allowed : 0.75 % Favored : 98.66 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.19), residues: 1586 helix: -2.52 (0.16), residues: 794 sheet: -3.42 (0.41), residues: 134 loop : -3.47 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 340 TYR 0.025 0.002 TYR A 122 PHE 0.087 0.003 PHE A 156 TRP 0.021 0.003 TRP A 920 HIS 0.020 0.002 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.01143 / 0.49 (13026) covalent geometry : angle 1.10636 / 0.58 (17628) SS BOND : bond 0.00131 / 0.07 ( 1) SS BOND : angle 3.61280 / 1.99 ( 2) hydrogen bonds : bond 0.21888 / 14.42 ( 422) hydrogen bonds : angle 7.04624 / 4.89 ( 1224) link_NAG-ASN : bond 0.00678 / 0.32 ( 2) link_NAG-ASN : angle 5.89162 / 2.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.487 Fit side-chains REVERT: A 377 PHE cc_start: 0.8685 (t80) cc_final: 0.8337 (t80) REVERT: A 398 TRP cc_start: 0.8003 (m100) cc_final: 0.7245 (m-10) REVERT: A 1019 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.6034 (t80) REVERT: A 1030 ARG cc_start: 0.6702 (tmm160) cc_final: 0.6480 (tmm-80) REVERT: A 1095 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6211 (tpt170) REVERT: A 1231 MET cc_start: 0.7807 (tpp) cc_final: 0.7469 (ttm) REVERT: A 1310 MET cc_start: 0.8552 (mtm) cc_final: 0.8296 (mtm) outliers start: 8 outliers final: 5 residues processed: 168 average time/residue: 0.1270 time to fit residues: 29.9204 Evaluate side-chains 138 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1240 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1490 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.101734 restraints weight = 17630.600| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.17 r_work: 0.2812 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13029 Z= 0.129 Angle : 0.716 12.511 17636 Z= 0.360 Chirality : 0.044 0.271 1981 Planarity : 0.005 0.072 2216 Dihedral : 11.531 167.083 1841 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.95 % Favored : 90.67 % Rotamer: Outliers : 1.34 % Allowed : 7.69 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.19), residues: 1586 helix: -1.95 (0.17), residues: 802 sheet: -3.14 (0.40), residues: 149 loop : -3.15 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1212 TYR 0.029 0.001 TYR A1283 PHE 0.056 0.001 PHE A 156 TRP 0.022 0.001 TRP A 923 HIS 0.007 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (13026) covalent geometry : angle 0.70803 / 0.36 (17628) SS BOND : bond 0.00301 / 0.16 ( 1) SS BOND : angle 2.65630 / 1.53 ( 2) hydrogen bonds : bond 0.04243 / 2.77 ( 422) hydrogen bonds : angle 4.61860 / 3.23 ( 1224) link_NAG-ASN : bond 0.00925 / 0.45 ( 2) link_NAG-ASN : angle 5.61154 / 2.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.489 Fit side-chains REVERT: A 370 LYS cc_start: 0.8747 (mttt) cc_final: 0.8176 (mptt) REVERT: A 387 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8950 (mt) REVERT: A 398 TRP cc_start: 0.8000 (m100) cc_final: 0.6939 (m-10) REVERT: A 957 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8152 (ttp80) REVERT: A 1019 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.5773 (t80) REVERT: A 1030 ARG cc_start: 0.6056 (tmm160) cc_final: 0.5751 (tmm-80) REVERT: A 1231 MET cc_start: 0.8374 (tpp) cc_final: 0.7372 (ttm) REVERT: A 1240 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6182 (tt0) REVERT: A 1686 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8133 (tm-30) outliers start: 18 outliers final: 10 residues processed: 171 average time/residue: 0.1200 time to fit residues: 29.6760 Evaluate side-chains 150 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1240 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.097191 restraints weight = 17952.695| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.27 r_work: 0.2722 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13029 Z= 0.246 Angle : 0.749 12.729 17636 Z= 0.374 Chirality : 0.048 0.265 1981 Planarity : 0.005 0.075 2216 Dihedral : 11.174 169.391 1837 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.73 % Favored : 87.96 % Rotamer: Outliers : 2.99 % Allowed : 10.31 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.20), residues: 1586 helix: -1.67 (0.17), residues: 810 sheet: -3.02 (0.42), residues: 134 loop : -3.11 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 838 TYR 0.017 0.002 TYR A 396 PHE 0.034 0.002 PHE A 156 TRP 0.025 0.002 TRP A 923 HIS 0.006 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.25 (13026) covalent geometry : angle 0.74276 / 0.37 (17628) SS BOND : bond 0.00788 / 0.41 ( 1) SS BOND : angle 2.23043 / 1.18 ( 2) hydrogen bonds : bond 0.05227 / 3.35 ( 422) hydrogen bonds : angle 4.48324 / 3.11 ( 1224) link_NAG-ASN : bond 0.00813 / 0.39 ( 2) link_NAG-ASN : angle 5.30815 / 1.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.495 Fit side-chains REVERT: A 220 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7501 (mtm-85) REVERT: A 370 LYS cc_start: 0.8880 (mttt) cc_final: 0.8524 (mtmm) REVERT: A 387 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8999 (mt) REVERT: A 398 TRP cc_start: 0.7980 (m100) cc_final: 0.6870 (m-10) REVERT: A 430 MET cc_start: 0.7833 (mtm) cc_final: 0.7628 (mtm) REVERT: A 957 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8179 (ttp80) REVERT: A 1019 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.5909 (t80) REVERT: A 1030 ARG cc_start: 0.6179 (tmm160) cc_final: 0.5915 (tmm-80) REVERT: A 1065 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6653 (pt) REVERT: A 1095 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6122 (tpt170) REVERT: A 1172 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7030 (p90) REVERT: A 1231 MET cc_start: 0.8559 (tpp) cc_final: 0.7383 (ttm) REVERT: A 1240 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6309 (tt0) REVERT: A 1433 GLU cc_start: 0.8569 (tp30) cc_final: 0.8194 (tp30) REVERT: A 1686 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8420 (tm-30) outliers start: 40 outliers final: 22 residues processed: 168 average time/residue: 0.1300 time to fit residues: 30.8634 Evaluate side-chains 155 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1229 THR Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1656 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 108 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 46 optimal weight: 0.0000 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 412 ASN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102572 restraints weight = 17732.379| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.21 r_work: 0.2838 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13029 Z= 0.106 Angle : 0.630 12.456 17636 Z= 0.313 Chirality : 0.041 0.213 1981 Planarity : 0.005 0.071 2216 Dihedral : 10.662 171.162 1835 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.39 % Favored : 91.30 % Rotamer: Outliers : 2.46 % Allowed : 12.99 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.20), residues: 1586 helix: -1.18 (0.18), residues: 799 sheet: -2.51 (0.42), residues: 131 loop : -2.99 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1401 TYR 0.018 0.001 TYR A1287 PHE 0.025 0.001 PHE A 156 TRP 0.023 0.001 TRP A 923 HIS 0.006 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (13026) covalent geometry : angle 0.62302 / 0.31 (17628) SS BOND : bond 0.00717 / 0.38 ( 1) SS BOND : angle 1.18143 / 0.62 ( 2) hydrogen bonds : bond 0.03307 / 2.15 ( 422) hydrogen bonds : angle 4.14128 / 2.88 ( 1224) link_NAG-ASN : bond 0.00870 / 0.42 ( 2) link_NAG-ASN : angle 5.08293 / 1.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.505 Fit side-chains REVERT: A 220 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7429 (mtm-85) REVERT: A 370 LYS cc_start: 0.8803 (mttt) cc_final: 0.8565 (mtpp) REVERT: A 387 ILE cc_start: 0.9288 (mm) cc_final: 0.9019 (mt) REVERT: A 398 TRP cc_start: 0.7949 (m100) cc_final: 0.6882 (m-10) REVERT: A 1019 PHE cc_start: 0.6605 (OUTLIER) cc_final: 0.5951 (t80) REVERT: A 1030 ARG cc_start: 0.6072 (tmm160) cc_final: 0.5814 (tmm-80) REVERT: A 1065 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6666 (pt) REVERT: A 1095 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.5925 (tpt170) REVERT: A 1172 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.6716 (p90) REVERT: A 1231 MET cc_start: 0.8452 (tpp) cc_final: 0.7380 (ttm) REVERT: A 1433 GLU cc_start: 0.8617 (tp30) cc_final: 0.8224 (tp30) REVERT: A 1686 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8381 (tm-30) outliers start: 33 outliers final: 19 residues processed: 182 average time/residue: 0.1240 time to fit residues: 32.3726 Evaluate side-chains 164 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 18 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.133414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.098176 restraints weight = 17904.335| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.32 r_work: 0.2736 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13029 Z= 0.212 Angle : 0.699 12.509 17636 Z= 0.347 Chirality : 0.045 0.204 1981 Planarity : 0.005 0.065 2216 Dihedral : 10.652 179.512 1832 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.53 % Favored : 89.09 % Rotamer: Outliers : 3.06 % Allowed : 13.52 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.21), residues: 1586 helix: -1.17 (0.18), residues: 806 sheet: -2.51 (0.45), residues: 127 loop : -2.99 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1081 TYR 0.015 0.001 TYR A 119 PHE 0.024 0.002 PHE A 156 TRP 0.022 0.002 TRP A 923 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.21 (13026) covalent geometry : angle 0.69337 / 0.35 (17628) SS BOND : bond 0.00575 / 0.30 ( 1) SS BOND : angle 1.18207 / 0.62 ( 2) hydrogen bonds : bond 0.04440 / 2.83 ( 422) hydrogen bonds : angle 4.20949 / 2.92 ( 1224) link_NAG-ASN : bond 0.00798 / 0.38 ( 2) link_NAG-ASN : angle 4.88332 / 1.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.471 Fit side-chains REVERT: A 220 ARG cc_start: 0.7866 (mtm-85) cc_final: 0.7420 (mtm-85) REVERT: A 370 LYS cc_start: 0.8857 (mttt) cc_final: 0.8421 (mtmm) REVERT: A 387 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9023 (mt) REVERT: A 398 TRP cc_start: 0.7912 (m100) cc_final: 0.6828 (m-10) REVERT: A 430 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7387 (mpp) REVERT: A 1019 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.6023 (t80) REVERT: A 1030 ARG cc_start: 0.6112 (tmm160) cc_final: 0.5844 (tmm-80) REVERT: A 1065 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6762 (pt) REVERT: A 1095 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6022 (tpt170) REVERT: A 1099 ASP cc_start: 0.9306 (OUTLIER) cc_final: 0.9049 (t0) REVERT: A 1172 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.6920 (p90) REVERT: A 1231 MET cc_start: 0.8462 (tpp) cc_final: 0.7366 (ttm) REVERT: A 1433 GLU cc_start: 0.8721 (tp30) cc_final: 0.8394 (tp30) REVERT: A 1621 GLN cc_start: 0.8533 (mm-40) cc_final: 0.7902 (pt0) REVERT: A 1686 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8395 (tm-30) outliers start: 41 outliers final: 24 residues processed: 161 average time/residue: 0.1258 time to fit residues: 29.1144 Evaluate side-chains 160 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1656 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 33 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 chunk 86 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 108 optimal weight: 0.0970 chunk 122 optimal weight: 0.0370 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103426 restraints weight = 17637.732| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.29 r_work: 0.2858 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13029 Z= 0.104 Angle : 0.613 12.370 17636 Z= 0.303 Chirality : 0.040 0.170 1981 Planarity : 0.004 0.065 2216 Dihedral : 10.138 175.129 1826 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.39 % Favored : 91.30 % Rotamer: Outliers : 2.84 % Allowed : 14.56 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.21), residues: 1586 helix: -0.74 (0.19), residues: 790 sheet: -2.02 (0.44), residues: 142 loop : -2.96 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 957 TYR 0.012 0.001 TYR A 82 PHE 0.017 0.001 PHE A 156 TRP 0.023 0.001 TRP A 923 HIS 0.007 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (13026) covalent geometry : angle 0.60691 / 0.30 (17628) SS BOND : bond 0.00643 / 0.34 ( 1) SS BOND : angle 0.87748 / 0.47 ( 2) hydrogen bonds : bond 0.02875 / 1.85 ( 422) hydrogen bonds : angle 3.99128 / 2.78 ( 1224) link_NAG-ASN : bond 0.00857 / 0.41 ( 2) link_NAG-ASN : angle 4.74017 / 1.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.509 Fit side-chains REVERT: A 155 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7022 (ttm-80) REVERT: A 370 LYS cc_start: 0.8826 (mttt) cc_final: 0.8181 (mptt) REVERT: A 387 ILE cc_start: 0.9313 (mm) cc_final: 0.9061 (mt) REVERT: A 398 TRP cc_start: 0.7859 (m100) cc_final: 0.6691 (m-10) REVERT: A 595 TYR cc_start: 0.8057 (m-10) cc_final: 0.7814 (m-10) REVERT: A 644 GLU cc_start: 0.7581 (mp0) cc_final: 0.7095 (mp0) REVERT: A 666 SER cc_start: 0.7609 (OUTLIER) cc_final: 0.7276 (m) REVERT: A 1019 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.5957 (t80) REVERT: A 1030 ARG cc_start: 0.6027 (tmm160) cc_final: 0.5768 (tmm-80) REVERT: A 1065 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6692 (pt) REVERT: A 1095 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.5953 (tpt170) REVERT: A 1099 ASP cc_start: 0.9281 (OUTLIER) cc_final: 0.9036 (t0) REVERT: A 1172 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.6664 (p90) REVERT: A 1231 MET cc_start: 0.8404 (tpp) cc_final: 0.7323 (ttm) REVERT: A 1433 GLU cc_start: 0.8741 (tp30) cc_final: 0.8456 (tp30) REVERT: A 1686 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8383 (tm-30) outliers start: 38 outliers final: 22 residues processed: 189 average time/residue: 0.1227 time to fit residues: 33.5203 Evaluate side-chains 175 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 114 optimal weight: 0.0670 chunk 133 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 85 optimal weight: 0.1980 chunk 141 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.099868 restraints weight = 17590.637| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.15 r_work: 0.2942 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13029 Z= 0.101 Angle : 0.613 11.413 17636 Z= 0.301 Chirality : 0.041 0.168 1981 Planarity : 0.004 0.061 2216 Dihedral : 9.885 174.357 1826 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.76 % Favored : 90.98 % Rotamer: Outliers : 2.84 % Allowed : 15.31 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.21), residues: 1586 helix: -0.46 (0.19), residues: 793 sheet: -1.89 (0.44), residues: 142 loop : -2.90 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1011 TYR 0.014 0.001 TYR A 119 PHE 0.016 0.001 PHE A 235 TRP 0.023 0.001 TRP A 923 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (13026) covalent geometry : angle 0.60706 / 0.30 (17628) SS BOND : bond 0.00511 / 0.27 ( 1) SS BOND : angle 0.87923 / 0.46 ( 2) hydrogen bonds : bond 0.02904 / 1.86 ( 422) hydrogen bonds : angle 3.87718 / 2.69 ( 1224) link_NAG-ASN : bond 0.00806 / 0.39 ( 2) link_NAG-ASN : angle 4.54151 / 1.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.449 Fit side-chains REVERT: A 86 HIS cc_start: 0.7247 (p-80) cc_final: 0.6948 (p90) REVERT: A 136 GLU cc_start: 0.5978 (OUTLIER) cc_final: 0.5741 (mp0) REVERT: A 155 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7117 (ttm-80) REVERT: A 370 LYS cc_start: 0.8868 (mttt) cc_final: 0.8504 (mtpp) REVERT: A 387 ILE cc_start: 0.9330 (mm) cc_final: 0.9088 (mt) REVERT: A 398 TRP cc_start: 0.7833 (m100) cc_final: 0.7083 (m-10) REVERT: A 644 GLU cc_start: 0.7608 (mp0) cc_final: 0.7144 (mp0) REVERT: A 1019 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6170 (t80) REVERT: A 1030 ARG cc_start: 0.6191 (tmm160) cc_final: 0.5927 (tmm-80) REVERT: A 1065 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6722 (pt) REVERT: A 1095 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.5945 (tpt170) REVERT: A 1099 ASP cc_start: 0.9247 (OUTLIER) cc_final: 0.9010 (t0) REVERT: A 1172 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.6578 (p90) REVERT: A 1231 MET cc_start: 0.8342 (tpp) cc_final: 0.7366 (ttm) REVERT: A 1392 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6810 (pp30) REVERT: A 1433 GLU cc_start: 0.8732 (tp30) cc_final: 0.8454 (tp30) REVERT: A 1686 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8388 (tm-30) outliers start: 38 outliers final: 19 residues processed: 184 average time/residue: 0.1248 time to fit residues: 32.8877 Evaluate side-chains 172 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1392 GLN Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 15 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 92 optimal weight: 0.1980 chunk 71 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 153 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.099944 restraints weight = 17457.976| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.15 r_work: 0.2950 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13029 Z= 0.104 Angle : 0.609 11.492 17636 Z= 0.298 Chirality : 0.041 0.165 1981 Planarity : 0.004 0.061 2216 Dihedral : 9.719 175.918 1826 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.58 % Favored : 91.17 % Rotamer: Outliers : 2.84 % Allowed : 15.68 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.21), residues: 1586 helix: -0.30 (0.19), residues: 792 sheet: -1.80 (0.44), residues: 143 loop : -2.83 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1011 TYR 0.012 0.001 TYR A 396 PHE 0.014 0.001 PHE A 235 TRP 0.023 0.001 TRP A 923 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (13026) covalent geometry : angle 0.60385 / 0.30 (17628) SS BOND : bond 0.00527 / 0.28 ( 1) SS BOND : angle 0.89473 / 0.47 ( 2) hydrogen bonds : bond 0.02925 / 1.87 ( 422) hydrogen bonds : angle 3.84084 / 2.67 ( 1224) link_NAG-ASN : bond 0.00787 / 0.38 ( 2) link_NAG-ASN : angle 4.41322 / 1.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.532 Fit side-chains REVERT: A 86 HIS cc_start: 0.7219 (p-80) cc_final: 0.6934 (p90) REVERT: A 136 GLU cc_start: 0.5896 (OUTLIER) cc_final: 0.5684 (mp0) REVERT: A 370 LYS cc_start: 0.8865 (mttt) cc_final: 0.8497 (mtmm) REVERT: A 387 ILE cc_start: 0.9332 (mm) cc_final: 0.9095 (mt) REVERT: A 398 TRP cc_start: 0.7813 (m100) cc_final: 0.7118 (m-10) REVERT: A 643 GLU cc_start: 0.7793 (pm20) cc_final: 0.7502 (pm20) REVERT: A 644 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: A 666 SER cc_start: 0.7667 (OUTLIER) cc_final: 0.7381 (m) REVERT: A 813 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8889 (tt) REVERT: A 1019 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6240 (t80) REVERT: A 1030 ARG cc_start: 0.6180 (tmm160) cc_final: 0.5907 (tmm-80) REVERT: A 1065 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6632 (pt) REVERT: A 1095 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.5942 (tpt170) REVERT: A 1099 ASP cc_start: 0.9251 (OUTLIER) cc_final: 0.9018 (t0) REVERT: A 1172 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.6625 (p90) REVERT: A 1231 MET cc_start: 0.8267 (tpp) cc_final: 0.7341 (ttm) REVERT: A 1392 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6882 (pp30) REVERT: A 1433 GLU cc_start: 0.8732 (tp30) cc_final: 0.8425 (tp30) REVERT: A 1686 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8384 (tm-30) outliers start: 38 outliers final: 23 residues processed: 178 average time/residue: 0.1328 time to fit residues: 33.6386 Evaluate side-chains 182 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain A residue 1392 GLN Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 52 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 145 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 91 optimal weight: 0.0060 chunk 128 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107199 restraints weight = 17671.603| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.09 r_work: 0.2920 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13029 Z= 0.100 Angle : 0.606 12.681 17636 Z= 0.295 Chirality : 0.041 0.162 1981 Planarity : 0.004 0.059 2216 Dihedral : 9.495 178.306 1826 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.20 % Favored : 91.55 % Rotamer: Outliers : 2.84 % Allowed : 15.76 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.22), residues: 1586 helix: -0.11 (0.19), residues: 793 sheet: -1.66 (0.45), residues: 143 loop : -2.79 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 957 TYR 0.011 0.001 TYR A 396 PHE 0.010 0.001 PHE A 349 TRP 0.023 0.001 TRP A 923 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (13026) covalent geometry : angle 0.60039 / 0.29 (17628) SS BOND : bond 0.00461 / 0.24 ( 1) SS BOND : angle 0.82983 / 0.44 ( 2) hydrogen bonds : bond 0.02787 / 1.78 ( 422) hydrogen bonds : angle 3.79136 / 2.64 ( 1224) link_NAG-ASN : bond 0.00776 / 0.37 ( 2) link_NAG-ASN : angle 4.29895 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.473 Fit side-chains REVERT: A 86 HIS cc_start: 0.7192 (p-80) cc_final: 0.6944 (p90) REVERT: A 251 ILE cc_start: 0.8344 (mt) cc_final: 0.8135 (mm) REVERT: A 370 LYS cc_start: 0.8902 (mttt) cc_final: 0.8578 (mtmm) REVERT: A 387 ILE cc_start: 0.9354 (mm) cc_final: 0.9119 (mt) REVERT: A 398 TRP cc_start: 0.7793 (m100) cc_final: 0.7088 (m-10) REVERT: A 643 GLU cc_start: 0.7811 (pm20) cc_final: 0.7437 (pm20) REVERT: A 644 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: A 666 SER cc_start: 0.7689 (OUTLIER) cc_final: 0.7429 (m) REVERT: A 970 PHE cc_start: 0.8104 (p90) cc_final: 0.7891 (p90) REVERT: A 1019 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.6142 (t80) REVERT: A 1030 ARG cc_start: 0.6199 (tmm160) cc_final: 0.5923 (tmm-80) REVERT: A 1065 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6622 (pt) REVERT: A 1075 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7502 (p) REVERT: A 1095 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6003 (tpt170) REVERT: A 1231 MET cc_start: 0.8297 (tpp) cc_final: 0.7421 (ttm) REVERT: A 1392 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6869 (pp30) REVERT: A 1433 GLU cc_start: 0.8722 (tp30) cc_final: 0.8425 (tp30) REVERT: A 1621 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7756 (pm20) REVERT: A 1686 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8375 (tm-30) outliers start: 38 outliers final: 21 residues processed: 186 average time/residue: 0.1231 time to fit residues: 32.9443 Evaluate side-chains 182 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain A residue 1392 GLN Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 9 optimal weight: 5.9990 chunk 158 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 138 optimal weight: 0.0000 chunk 114 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 135 optimal weight: 0.0570 overall best weight: 0.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS A 985 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.105387 restraints weight = 17529.875| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.12 r_work: 0.2886 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13029 Z= 0.097 Angle : 0.600 11.514 17636 Z= 0.293 Chirality : 0.040 0.152 1981 Planarity : 0.004 0.060 2216 Dihedral : 9.230 178.886 1826 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.07 % Favored : 91.68 % Rotamer: Outliers : 2.61 % Allowed : 16.28 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.22), residues: 1586 helix: 0.01 (0.19), residues: 799 sheet: -1.60 (0.44), residues: 143 loop : -2.78 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 957 TYR 0.010 0.001 TYR A 82 PHE 0.009 0.001 PHE A1007 TRP 0.026 0.001 TRP A 923 HIS 0.018 0.001 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (13026) covalent geometry : angle 0.59539 / 0.29 (17628) SS BOND : bond 0.00436 / 0.23 ( 1) SS BOND : angle 0.76123 / 0.40 ( 2) hydrogen bonds : bond 0.02636 / 1.68 ( 422) hydrogen bonds : angle 3.75155 / 2.61 ( 1224) link_NAG-ASN : bond 0.00754 / 0.36 ( 2) link_NAG-ASN : angle 4.17757 / 1.47 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 86 HIS cc_start: 0.7145 (p-80) cc_final: 0.6922 (p90) REVERT: A 251 ILE cc_start: 0.8300 (mt) cc_final: 0.8090 (mm) REVERT: A 370 LYS cc_start: 0.8819 (mttt) cc_final: 0.8471 (mtmm) REVERT: A 387 ILE cc_start: 0.9303 (mm) cc_final: 0.9075 (mt) REVERT: A 398 TRP cc_start: 0.7753 (m100) cc_final: 0.7032 (m-10) REVERT: A 430 MET cc_start: 0.8056 (mpp) cc_final: 0.7762 (mpp) REVERT: A 643 GLU cc_start: 0.7864 (pm20) cc_final: 0.7519 (pm20) REVERT: A 644 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: A 666 SER cc_start: 0.7772 (OUTLIER) cc_final: 0.7489 (m) REVERT: A 1019 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6141 (t80) REVERT: A 1065 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6564 (pt) REVERT: A 1095 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.5865 (tpt170) REVERT: A 1172 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.6498 (p90) REVERT: A 1231 MET cc_start: 0.8299 (tpp) cc_final: 0.7354 (ttm) REVERT: A 1392 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6850 (pp30) REVERT: A 1433 GLU cc_start: 0.8717 (tp30) cc_final: 0.8365 (tp30) REVERT: A 1621 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7810 (pm20) REVERT: A 1686 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8334 (tm-30) outliers start: 35 outliers final: 24 residues processed: 180 average time/residue: 0.1272 time to fit residues: 32.7583 Evaluate side-chains 182 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain A residue 1392 GLN Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 31 optimal weight: 2.9990 chunk 133 optimal weight: 0.0270 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 0.0020 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 103 optimal weight: 0.6980 chunk 122 optimal weight: 0.0020 chunk 114 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106699 restraints weight = 17518.395| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.23 r_work: 0.2899 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13029 Z= 0.096 Angle : 0.605 14.969 17636 Z= 0.292 Chirality : 0.040 0.144 1981 Planarity : 0.004 0.059 2216 Dihedral : 8.769 174.319 1826 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.82 % Favored : 92.06 % Rotamer: Outliers : 2.32 % Allowed : 16.50 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.22), residues: 1586 helix: 0.28 (0.20), residues: 797 sheet: -1.53 (0.44), residues: 143 loop : -2.71 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1655 TYR 0.012 0.001 TYR A 122 PHE 0.037 0.001 PHE A1007 TRP 0.024 0.001 TRP A 923 HIS 0.013 0.001 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (13026) covalent geometry : angle 0.60060 / 0.29 (17628) SS BOND : bond 0.00363 / 0.19 ( 1) SS BOND : angle 0.64827 / 0.34 ( 2) hydrogen bonds : bond 0.02335 / 1.50 ( 422) hydrogen bonds : angle 3.67811 / 2.55 ( 1224) link_NAG-ASN : bond 0.00744 / 0.36 ( 2) link_NAG-ASN : angle 4.07429 / 1.43 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3429.95 seconds wall clock time: 59 minutes 29.45 seconds (3569.45 seconds total)